WooCommerce installs some custom tables to store its data during install. More about tables installed: https://github.com/woocommerce/woocommerce/wiki/Database-Description
Tables can be removed when uninstalling WooCommerce, not during deactivation. This doesn’t happen automatically. To delete the WooCommerce tables from the database entirely, follow the instructions at Uninstalling WooCommerce.
Note: When defining a WordPress SQL table prefix, make sure it’s less than 20 characters. Otherwise WooCommerce is unable to create all tables properly. This could lead to the following issue.